Update AF_comparison.R

WES/AF_comparison.R

@@ -9,7 +9,6 @@ inputdata <- list()
 for (mysample in c("12_27_1","12_27_2", "10_395_3", "10_395_4")) {
   
   inputdata[["rawcall"]][[mysample]] <- filter_variants_v3(infile = paste0(mysample, "_dbsnp_cc_cnc_dbnsfp_refseq_light_raw_filtered.fields.txt"), sampleid = mysample, dp = 50)
-  inputdata[["passonly"]][[mysample]] <- filter_variants_v3(infile = paste0(mysample, "_dbsnp_cc_cnc_dbnsfp_refseq_light.fields.txt"), sampleid = mysample, dp = 50)
 }
 
 source(file = "Compare_variants_AF_v3.R")
@@ -70,48 +69,6 @@ plot_grid(AF_density_raw[["12-27_miRNA_L"]], AF_density_raw[["12-27_miRNA_H"]],
           nrow = 2)
 dev.off()
 
-## PLOTTING PASS-ONLY
-
-tmpdf_1_pass <- subset.data.frame(x = Comparison_12_27$passonly$unionannot, select = c("AF_GFP_H"), subset = AF_GFP_H > 0)
-tmpdf_2_pass <- subset.data.frame(x = Comparison_12_27$passonly$unionannot, select = c("AF_GFP_L"), subset = AF_GFP_L > 0)
-
-tmpdf_3_pass <- subset.data.frame(x = Comparison_10_395$passonly$unionannot, select = c("AF_GFP_H"), subset = AF_GFP_H > 0)
-tmpdf_4_pass <- subset.data.frame(x = Comparison_10_395$passonly$unionannot, select = c("AF_GFP_L"), subset = AF_GFP_L > 0)
-
-AF_density_pass <- list()
-
-AF_density_pass[["12-27_miRNA_L"]] <- ggplot(data = tmpdf_1_pass,
-                                        mapping = aes(AF_GFP_H)) + ylim(0,300) +
-  geom_histogram(bins = 50, fill = alpha("#003366",0.8)) + xlab("miRNA_low") +
-  theme(axis.text = element_text(size = 14), legend.title = element_blank()) +
-  ggtitle("12-27_miRNA_L")
-
-AF_density_pass[["12-27_miRNA_H"]] <- ggplot(data = tmpdf_2_pass,
-                                        mapping = aes(AF_GFP_L)) + ylim(0,300) +
-  geom_histogram(bins = 50, fill = alpha("#fc2803",0.8))+ xlab("miRNA_high") +
-  theme(axis.text = element_text(size = 14), legend.title = element_blank()) +
-  ggtitle("12-27_miRNA_H")
-
-AF_density_pass[["10-395_miRNA_L"]] <- ggplot(data = tmpdf_3_pass,
-                                         mapping = aes(AF_GFP_H)) + ylim(0,300) +
-  geom_histogram(bins = 50, fill = alpha("#003366",0.8)) + xlab("miRNA_low") +
-  theme(axis.text = element_text(size = 14), legend.title = element_blank()) +
-  ggtitle("10-395_miRNA_L")
-
-AF_density_pass[["10-395_miRNA_H"]] <- ggplot(data = tmpdf_4_pass,
-                                         mapping = aes(AF_GFP_L)) + ylim(0,300) +
-  geom_histogram(bins = 50, fill = alpha("#fc2803",0.8)) + xlab("miRNA_high") +
-  theme(axis.text = element_text(size = 14), legend.title = element_blank()) +
-  ggtitle("10-395_miRNA_H")
-
-png(filename = "AF_density_pass_variants.png", width = 8, height = 6, units = "in", res = 300)
-plot_grid(AF_density_pass[["12-27_miRNA_L"]], AF_density_pass[["12-27_miRNA_H"]],
-          AF_density_pass[["10-395_miRNA_L"]] , AF_density_pass[["10-395_miRNA_H"]],
-          nrow = 2)
-dev.off()
-
-# Histograms with PASS or clustered_events
-
 AF_density_mildfilt <- list()
 Mild_vars_12_27 <- Comparison_12_27$rawcall$unionannot